SAN FRANCISCO -- With a major storm churning through the Bay Area on the busiest travel day of the season Friday, more than 100 flights in and out of San Francisco International Airport were canceled and travelers were delayed for hours, an airport spokesman said.

Flights that could get in and out of the airport were averaging delays of about three hours, duty manager Dan Dinnocenti said, because two of the airport's four runways were shut down.

Flights were expected to be delayed well into Saturday morning as the backlog slowly reduced, he said. "It will be 2 or 3 in the morning before we get caught up," he said.

Southwest Airlines passengers wait in long lines at San Francisco International Airport on Dec. 21, 2012. Lines were long at SFO due to weather problems in the Midwest. (John Green/Staff)

Earlier in the day, the cancellations mostly affected commuter short-haul flights up and down the West Coast, and were split between arrivals and departures, airport spokesman Doug Yakel said. Delays ranged from an hour to as long as three hours for some arriving flights throughout the day.

As always, travelers are advised to check with their airlines before heading to the airport to find out about delays or cancellations, Yakel said.

With an FAA-mandated traffic management program in place at SFO due to wind, rain and low cloud cover, the canceled flights act as a sort of relief valve, Yakel said. Fewer arriving and departing flights will mean fewer delays as landings and takeoffs are spaced farther apart.

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San Jose's Mineta International Airport had delays of 15 to 30 minutes by late afternoon, spokeswoman Rosemary Barnes said. They were mostly caused by a "domino effect" of delays caused by bad weather in the Midwest, she said.

A spokesman for Oakland International Airport said there were no major delays or weather-related cancellations late Friday afternoon.